CS 267 Applications of Parallel Computers Lecture 10: Sources of Parallelism and Locality

CS267 L10 Sources of Parallelism.1 Demmel Sp 1999

CS 267 Applications of Parallel Computers

Lecture 10:

Sources of Parallelism and Locality

James Demmel

http://www.cs.berkeley.edu/~demmel/cs267_Spr99


Recap: Parallel Models and Machines° Machine models Programming models

• shared memory - threads• distributed memory - message passing• SIMD - data parallel - shared address space

° Steps in creating a parallel program• decomposition

• assignment

• orchestration

• mapping

° Performance in parallel programs• try to minimize performance loss from

- load imbalance

- communication

- synchronization

- extra work


Outline

° Simulation models

° A model problem: sharks and fish

° Discrete event systems

° Particle systems

° Lumped systems (Ordinary Differential Equations, ODEs)

° (Next time: Partial Different Equations, PDEs)


Simulation Modelsand

A Simple Example


Sources of Parallelism and Locality in Simulation° Real world problems have parallelism and locality

• Many objects do not depend on other objects

• Objects often depend more on nearby than distant objects

• Dependence on distant objects often “simplifies”

° Scientific models may introduce more parallelism• When continuous problem is discretized, may limit effects to

timesteps

• Far-field effects may be ignored or approximated, if they have little effect

° Many problems exhibit parallelism at multiple levels• e.g., circuits can be simulated at many levels and within each

there may be parallelism within and between subcircuits


Basic Kinds of Simulation° Discrete event systems

• e.g.,”Game of Life”, timing level simulation for circuits

° Particle systems• e.g., billiard balls, semiconductor device simulation, galaxies

° Lumped variables depending on continuous parameters• ODEs, e.g., circuit simulation (Spice), structural mechanics, chemical

kinetics

° Continuous variables depending on continuous parameters• PDEs, e.g., heat, elasticity, electrostatics

° A given phenomenon can be modeled at multiple levels

° Many simulations combine these modeling techniques


A Model Problem: Sharks and Fish° Illustration of parallel programming

• Original version (discrete event only) proposed by Geoffrey Fox

• Called WATOR

° Basic idea: sharks and fish living in an ocean• rules for movement (discrete and continuous)

• breeding, eating, and death

• forces in the ocean

• forces between sea creatures

° 6 problems (S&F1 - S&F6)• Different sets of rule, to illustrate different phenomena

° Available in Matlab, Threads, MPI, Split-C, Titanium, CMF, CMMD, pSather • not all problems in all languages

° www.cs.berkeley.edu/~demmel/cs267/Sharks_and_Fish• being updated


Discrete Event Systems


Discrete Event Systems

° Systems are represented as• finite set of variables

• each variable can take on a finite number of values

• the set of all variable values at a given time is called the state

• each variable is updated by computing a transition function depending on the other variables

° System may be• synchronous: at each discrete timestep evaluate all transition

functions; also called a finite state machine

• asynchronous: transition functions are evaluated only if the inputs change, based on an “event” from another part of the system; also called event driven simulation

° E.g., functional level circuit simulation• state is represented by a set of boolean variables (high & low

voltages)

• set of logical rules defining state transitions (and, or, etc.)

• synchronous: only interested in state at clock ticks


Sharks and Fish as Discrete Event System

° Ocean modeled as a 2D toroidal grid

° Each cell occupied by at most one sea creature

° S&F3, 4 and 5 are variations on this


The Game of Life (Sharks and Fish 3)° Fish only, no sharks

° An new fish is born if• a cell is empty

• exactly 3 (of 8) neighbors contain fish

° A fish dies (of overcrowding) if• cell contains a fish

• 4 or more neighboring cells are full

° A fish dies (of loneliness) if• cell contains a fish

• less than 2 neighboring cells are full

° Other configurations are stable


Parallelism in Sharks and Fish

° The simulation is synchronous• use two copies of the grid (old and new)

• the value of each new grid cell depends only on 9 cells (itself plus 8 neighbors) in old grid

• simulation proceeds in timesteps, where each cell is updated at every timestep

° Easy to parallelize using domain decomposition

° Locality is achieved by using large patches of the ocean• boundary values from neighboring patches are needed

° If only cells next to occupied ones are visited (an optimization), then load balance is more difficult. The activities in this system are discrete events

P4

P1 P2 P3

P5 P6

P7 P8 P9

Repeat compute locally to update local system barrier() exchange state info with neighborsuntil done simulating


Parallelism in Synchronous Circuit Simulation° Circuit is a graph made up of subcircuits connected by wires

• component simulations need to interact if they share a wire

• data structure is irregular (graph)

• parallel algorithm is synchronous

- compute subcircuit outputs

- propagate outputs to other circuits

° Graph partitioning assigns subgraphs to processors• Determines parallelism and locality

• Want even distribution of nodes (load balance)

• With minimum edge crossing (minimize communication)

• Nodes and edges may both be weighted by cost

• NP-complete to partition optimally, but many good heuristics (later lectures)

edge crossings = 6 edge crossings = 10


Parallelism in Asynchronous Circuit Simulation° Synchronous simulations may waste time

• simulate even when the inputs do not change, little internal activity

• activity varies across circuit

° Asynchronous simulations update only when an event arrives from another component• no global timesteps, but events contain time stamp

• Ex: Circuit simulation with delays (events are gates changing)

• Ex: Traffic simulation (events are cars changing lanes, etc.)


Scheduling Asynchronous Circuit Simulation° Conservative:

• Only simulate up to (and including) the minimum time stamp of inputs

• May need deadlock detection if there are cycles in graph, or else “null messages”

• Ex: Pthor circuit simulator in Splash1 from Stanford

° Speculative: • Assume no new inputs will arrive and keep simulating, instead of waiting

• May need to backup if assumption wrong

• Ex: Parswec circuit simulator of Yelick/Wen

• Ex: Standard technique for CPUs to execute instructions

° Optimizing load balance and locality is difficult• Locality means putting tightly coupled subcircuit on one processor

• Since “active” part of circuit likely to be in a tightly coupled subcircuit, this may be bad for load balance


Particle Systems


Particle Systems

° A particle system has • a finite number of particles

• moving in space according to Newton’s Laws (i.e. F = ma)

• time is continuous

° Examples• stars in space with laws of gravity

• electron beam semiconductor manufacturing

• atoms in a molecule with electrostatic forces

• neutrons in a fission reactor

• cars on a freeway with Newton’s laws plus model of driver and engine

° Reminder: many simulations combine techniques such as particle simulations with some discrete events (Ex Sharks and Fish)


Forces in Particle Systems

° Force on each particle can be subdivided

° External force• ocean current to sharks and fish world (S&F 1)

• externally imposed electric field in electron beam

° Nearby force• sharks attracted to eat nearby fish (S&F 5)

• balls on a billiard table bounce off of each other

• Van der Wals forces in fluid (1/r^6)

° Far-field force• fish attract other fish by gravity-like (1/r^2 ) force (S&F 2)

• gravity, electrostatics, radiosity

• forces governed by elliptic PDE

force = external_force + nearby_force + far_field_force


Parallelism in External Forces° These are the simplest

° The force on each particle is independent

° Called “embarrassingly parallel”

° Evenly distribute particles on processors• Any distribution works

• Locality is not an issue, no communication

° For each particle on processor, apply the external force


Parallelism in Nearby Forces

° Nearby forces require interaction => communication

° Force may depend on other nearby particles• Ex: collisions

• simplest algorithm is O(n^2): look at all pairs to see if they collide

° Usual parallel model is domain decomposition of physical domain• O(n^2/p) particles per processor if evenly distributed

° Challenge 1: interactions of particles near processor boundary• need to communicate particles near boundary to neighboring processors

• surface to volume effect means low communication

• Which communicates less: squares (as below) or slabs?

° Challenge 2: load imbalance, if particles cluster• galaxies, electrons hitting a device wall

Need to check for collisions between regions


Load balance via Tree Decomposition° To reduce load imbalance, divide space unevenly

° Each region contains roughly equal number of particles

° Quad tree in 2D, Oct-tree in 3D

Example: each square contains at most 3 particles


Parallelism in Far-Field Forces° Far-field forces involve all-to-all interaction =>

communication

° Force depends on all other particles• Ex: gravity

• Simplest algorithm is O(n^2) as in S&F 2, 4, 5

• Just decomposing space does not help since every particle apparently needs to “visit” every other particle

° Use more clever algorithms to beat O(n^2)


Far-field forces: Particle-Mesh Methods° Superimpose a regular mesh

° “Move” particles to nearest grid point

° Exploit fact that far-field satisfies a PDE that is easy to solve on a regular mesh • FFT, Multigrid

• Wait for next lecture

° Accuracy depends on how fine the grid is and uniformity of particles


Far-field forces: Tree Decomposition

° Based on approximation

° O(n log n) or O(n) instead of O(n^2)

° Forces from group of far-away particles “simplifies” • They resemble a single larger particle

° Use tree; each node contains an approximation of descendents

° Several Algorithms• Barnes-Hut

• Fast Multipole Method (FMM) of Greengard/Rohklin

• Anderson

• Later lectures


Lumped SystemsODEs


System of Lumped Variables° Many systems approximated by

• System of “lumped” variables

• Each depends on continuous parameter (usually time)

° Example: circuit• approximate as graph

• wires are edges

• nodes are connections between 2 or more wires

• each edge has resistor, capacitor, inductor or voltage source

• system is “lumped” because we are not computing the voltage/current at every point in space along a wire, just endpoints

• Variables related by Ohm’s Law, Kirchoff’s Laws, etc.

° Form a system of Ordinary Differential Equations, ODEs


Circuit Example° State of the system is represented by

• v_n(t) node voltages

• i_b(t) branch currents all at time t

• v_b(t) branch voltages

° Equations include• Kirchoff’s current

• Kirchoff’s voltage

• Ohm’s law

• Capacitance

• Inductance

° Write as single large system of ODEs (possibly with constraints)

0 A 0 v_n 0

A’ 0 -I * i_b = S

0 R -I v_b 0

0 -I C*d/dt 0

0 L*d/dt I 0


Systems of Lumped Variables

° Another example is structural analysis in Civil Eng.• Variables are displacement of points in a building

• Newton’s and Hook’s (spring) laws apply

• Static modeling: exert force and determine displacement

• Dynamic modeling: apply continuous force (earthquake)

° The system in these case (and many) will be sparse• i.e., most array elements are 0

• neither store nor compute on these 0’s


Solving ODEs

° Explicit methods to compute solution(t)• Ex: Euler’s method

• Simple algorithm: sparse matrix vector multiply

• May need to take very small timesteps, especially if system is stiff (i.e. can change rapidly)

° Implicit methods to compute solution(t)• Ex: Backward Euler’s Method

• Larger timesteps, especially for stiff problems

• More difficult algorithm: solve a sparse linear system

° Computing modes of vibration• Finding eigenvalues and eigenvectors

• Ex: do resonant modes of building match earthquakes?

° All these reduce to sparse matrix problems• Explicit: sparse matrix-vector multiplication

• Implicit: solve a sparse linear system

- direct solvers (Gaussian elimination)

- iterative solvers (use sparse matrix-vector multiplication)

• Eigenvalue/vector algorithms may also be explicit or implicit


Parallelism in Sparse Matrix-vector multiplication° y = A*x, where A is sparse and n x n

° Questions• which processors store

- y[i], x[i], and A[i,j]

• which processors compute

- x[i] = sum from 1 to n or A[i,j] * x[j]

° Graph partitioning• Partition index set {1,…,n} = N1 u N2 u … u Np

• for all i in Nk, store y[i], x[i], and row i of A on processor k

• Processor k computes its own y[i]

° Constraints• balance load

• balance storage

• minimize communication


Graph Partitioning and Sparse Matrices

1 1 1 1

2 1 1 1 1

3 1 1 1

4 1 1 1 1

5 1 1 1 1

6 1 1 1 1

1 2 3 4 5 6

3

6

2

1

5

4

° Relationship between matrix and graph

° A “good” partition of the graph has• equal number of (weighted) nodes in each part (load balance)

• minimum number of edges crossing between (minimize communication)

° Can reorder the rows/columns of the matrix by putting all the nodes in one partition together


More on Matrix Reordering via Graph Partitioning° Goal is to reorder rows and columns to

• improve load balance

• decrease communication

° “Ideal” matrix structure for parallelism: (nearly) block diagonal• p (number of processors) blocks

• few non-zeros outside these blocks, since these require communication

= *

P0

P1

P2

P3

P4


What about implicit methods and eigenproblems?° Direct methods (Gaussian elimination)

• future lectures will consider both dense and sparse cases

° Iterative solvers• future lectures will discuss several of these

• most have sparse-matrix-vector multiplication in kernel

° Eigenproblems• future lectures will discuss dense and sparse cases

• depends on student interest

CS 267 Applications of Parallel Computers Lecture 10: Sources of Parallelism and Locality

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